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        <h1>Structure Checker</h1>

        <p>Structure checker is a tool for filtering drawing mistakes or special structural elements.
            Registering a compound in a company's database might limit the user in for example
            the introduction of non-natural isotopes, query bonds, species with charge etc.
            Structure checker runs a check on the molecule(s) features and lists
            them in a separate window, with the option to refresh when you make changes
            to your drawing. The Structure checker works with predefined checking elements and
            you can choose which ones should be considered when you run a check.
        <p> Structure checker's command line interface and API for batch usage requires
            a Standardizer Pro licence. This guide refers to the checker available free in
            MarvinSketch as an add-on.
            <p>
<a href="#abbr">abbreviated group</a> <a href="#alias">alias</a>
        <a href="#arom">aromaticity</a> <a href="#atommap">atom map</a>
        <a href="#atomvalue">atom value</a> <a href="#attached">attached data</a>
        <a href="#bondangle"> bond angle</a> <a href="#bondlength"> bond length</a>
        <a href="#chiralflag">chiral flag</a> <a href="#coord">coordination system</a>
        <a href="#crosseddouble">crossed double bond</a> <a href="#doublebond">double bond stereo</a>
        <a href="#explh">explicit hydrogen</a> <a href="#isotope">isotope</a>
        <a href="#missingatommap">missing atom map</a> <a href="#molcharge">molecule charge</a>
        <a href="#multicenter">multicenter</a> <a href="#overlappingatoms">overlapping atoms</a>
        <a href="#overlappingbonds">overlapping bonds</a> <a href="#pseudo">pseudo</a>
        <a href="#queryatom">query atom</a> <a href="#querybond">query bond</a>
        <a href="#radical">radical</a> <a href="#reactionmap">reaction map</a>
        <a href="#3d">3 dimension</a> <a href="#valence">valence</a>
        <a href="#wedge">wedge</a> <a href="#wigglydouble">wiggly double bond</a>

            <h2>Setting Structure Checker configuration</h2>
        <p>Before you start using the Stucture Checker, consult the list of
            available checkers in the Preferences dialog (Edit -&gt; Preferences -&gt; Checkers tab).
              <p><img src="pref_checkers.png" width="477" height="318" alt="pref_checkers"/>
        <p>The default list contains checkers in alphabetical order.
            Click on the name of the checker to see additional options and select the
            needed options by clicking the tick box.
        <p>Two types of checkers are listed: error detecting and feature detecting checkers.
            Error checkers are looking for chemically wrong molecule parts (e.g. valence errors,
            overlapping atoms), while the
            feature checkers searches the selected molecule characteristics which
            in the specific structures are not considered as an error (e.g. query properties). The
            two types are distincted by the addtional 'error' tag and different icons.
        <h3>Checking order</h3>
        Some molecule properties might change after fixing an isssue.
        You can define a checking sequence by moving up or down the list elements.
        The order of the checkers may be important in case you run a Fix all action.
        <br>To change the order of the checker items, select the checker from the
        list and click the up <img src="up.png" width="24" height="24" alt="up"/>
        or down <img src="down.png" width="24" height="24" alt="down"/>
        icon on the right side of the dialog.
        <h3>Add and remove checker items</h3>
        To discard items from the checking sequence, select the checker and click the
        <img src="remove.png" width="24" height="24" alt="remove"/>
        button on the right. To revert this modification or add new elements to the list, click
        the <img src="add.png" width="24" height="24" alt="add"/>
        button on the right and select the checker needed.

        <h3>Save and load checker lists</h3>
        Different checking lists might be needed for different compound families. To
        make checking simpler, you can save your checking list to your
        computer and open it again if you are editing the same molecule type. Click the
        Save button <img src="save.png" width="24" height="24" alt="save"/>
        to save your settings and click the Load button <img src="open.png" width="24" height="24" alt="open"/>
        to open a saved list.


        <h2>Usage</h2>
        <h3>Start Structure Checker</h3>
        You can open Structure Checker at any stage of your work. As you
        click the Check structure icon <img src="defaultcheck.png" width="24" height="24" alt="defaultcheck"/>
        in the toolbar or in the Structure menu or left-click the Checker button in the statusbar,
        a window will
        appear next to the sketching window. The molecule regions are highlighted
        on the canvas with a light red color. If you click on any checker
        message, the effected area changes color to darker red. If you move the cursor
        over one of the affected atoms or bonds, the appropriate checker message is highlighted
        in the checker list.

        <h3>Recheck the structure</h3>
        After you have changed the structure (including accepting a fix),
        the checker will offer re-checking. Click on the recheck icon
        in the Checker window. <img src="checkerwindow.png" width="255" height="317" alt="check"/>
        <p>At any point you can allow the Structure checker to fix the issues one
        by one or every of them by a single click. Another option is to turn on automatic rechecking: click the Enable
        automatic checking in the bottom of the text.

        <h3>Automatic structure checking</h3>
        Turn on Automatic checking to follow every drawing step you make by a quick check.
        This option is switched on in the Structure menu or right-clicking the Checker
        button on the status bar which then becomes colored. In case of an
        error a red exclamation mark appears.
        Left-clicking on this icon opens the Structure Checker window, where all the
        warnings are listed.
        <p>While the molecules are scanned for checker issues, a yellow question mark appears on the status bar.
        <p>If the molecule is correct, a green check mark appears in the Checker icon on the status bar.


        <h2>List of available checkers and fixers</h2>
        <a href="#abbr">abbreviated group</a> <a href="#alias">alias</a>
        <a href="#arom">aromaticity</a> <a href="#atommap">atom map</a>
        <a href="#atomvalue">atom value</a> <a href="#attached">attached data</a>
        <a href="#bondangle"> bond angle</a> <a href="#bondlength"> bond length</a>
        <a href="#chiralflag">chiral flag</a> <a href="#coord">coordination system</a>
        <a href="#crosseddouble">crossed double bond</a> <a href="#doublebond">double bond stereo</a>
        <a href="#explh">explicit hydrogen</a> <a href="#isotope">isotope</a>
        <a href="#missingatommap">missing atom map</a> <a href="#molcharge">molecule charge</a>
        <a href="#multicenter">multicenter</a> <a href="#overlappingatoms">overlapping atoms</a>
        <a href="#overlappingbonds">overlapping bonds</a> <a href="#pseudo">pseudo</a>
        <a href="#queryatom">query atom</a> <a href="#querybond">query bond</a>
        <a href="#radical">radical</a> <a href="#reactionmap">reaction map</a>
        <a href="#3d">3 dimension</a> <a href="#valence">valence</a>
        <a href="#wedge">wedge</a> <a href="#wigglydouble">wiggly double bond</a>



        <dl>
            <dt><a name="abbr" type="anchor"><b>Abbreviated Group</b></a></dt>
            <dd>
                <ul>
                    <li>Checker searches for abbreviated groups in the structure, contracted, expanded or both.
                    <li>Fixer offers ungrouping abbreviated groups; expanding abbreviated groups; contracting abbreviated groups.
                </ul>
                <br><b>Example</b>: ungroup a contracted and an expanded phenyl group.
                <table border="0">
                    <tbody>
                        <tr>
                            <td>Warning:</td>
                            <td><img src="ex_abbrev_ch.png" width="353" height="217" alt="ex_abbrev_ch"/></td>
                        </tr>
                        <tr>
                            <td>Fix:</td>
                            <td><img src="ex_abbrev_f.png" width="341" height="245" alt="ex_abbrev_f"/></td>
                        </tr>
                    </tbody>
                </table>
                Notes: If attachment point is not connected to any atom, ungrouping
                removes attachment points of the abbreviated group and adds an implicit hydrogen.
            </dd><br>

            <dt><a name="alias" type="anchor"><b>Alias</b></a></dt>
            <dd>
                <ul>
                    <li>Checker searches for aliases in the structure.
                    <li>Fixer offers converting the alias to atom if the alias value corresponds to an element (e.g. Ar);<br>
                        converting the alias to abbreviated group if the alias values corresponds to a group in the abbeviated group list; <br>
                        removing alias (revealing the atom under the alias);<br>
                        or deleting the alias atom.
                </ul>
                <br><b>Example</b>: convert a methoxy group defined as an alias to an abbreviated group.
                <table border="0">
                    <tbody>
                        <tr>
                            <td>Warning:</td>
                            <td><img src="ex_alias_ch.png" width="159" height="153" alt="ex_alias_ch"/></td>
                        </tr>
                        <tr>
                            <td>Fix:</td>
                            <td><img src="ex_alias_f.png" width="149" height="145" alt="ex_alias_f"/></td>
                        </tr>
                    </tbody>
                </table>
                Note: The abbreviated group is linked correctly to the chain after the fix, i.e. bond through the oxygen atom.
                <br>
                <br><b>Example</b>: remove the NH<sub>2</sub> alias from the carbon atom.
                <table border="0">
                    <tbody>
                        <tr>
                            <td>Warning:</td>
                            <td><img src="ex_alias2_ch.png" width="94" height="112" alt="ex_alias2_ch"/></td>
                        </tr>
                        <tr>
                            <td>Fix:</td>
                            <td><img src="ex_alias2_f.png" width="85" height="94" alt="ex_alias2_f"/></td>
                        </tr>
                    </tbody>
                </table>
                Note: alias only covers the atom, and fixer removes this alias from the original atom.

            </dd><br>

            <dt><a name="arom" type="anchor"><b>Aromaticity</b></a></dt>
            <dd>
                <ul>
                    <li>Checker searches for aromatic systems that can't be
                        dearomatized or rearomatizing with the given method does not reproduce the initial molecule.
                        <br>Options: choice between basic, general or loose aromatization methods.
                    <li>Fixer offers rearomatizing or dearomatizing the aromatic system.
                </ul>
                <br><b>Example</b>: the 2-pyridone aromatized in general mode is corrected after a checking of aromatization in basic mode.
                <table border="0">
                    <tbody>
                        <tr>
                            <td>Warning:</td>
                            <td><img src="ex_arom_ch.png" width="150" height="181" alt="ex_arom_ch"/></td>
                        </tr>
                        <tr>
                            <td>Fix:</td>
                            <td><img src="ex_arom_f.png" width="135" height="180" alt="ex_arom_f"/></td>
                        </tr>
                    </tbody>
                </table>
                Notes: In this case, both rearomatization and dearomatization fix yields the same structure.<br>
                <a href="../sci/aromatization-doc.html">Details on aromaticity detection.</a>
            </dd>
            <br>


            </dd>
            <dt><a name="atommap" type="anchor"><b>Atom Map</b></a></dt>
            <dd><ul>
                    <li>Checker searches for atom maps.
                    <li>Fixer offers removing atom maps.
                </ul>
                <br><b>Example</b>: remove atom map from a partially mapped ethyl methylether molecule.
                <table border="0">
                    <tbody>
                        <tr>
                            <td>Warning:</td>
                            <td><img src="ex_atommap_ch.png" width="173" height="90" alt="ex_atommap_ch"/></td>
                        </tr>
                        <tr>
                            <td>Fix:</td>
                            <td><img src="ex_atommap_f.png" width="150" height="82" alt="ex_atommap_f"/></td>
                        </tr>
                    </tbody>
                </table>
            </dd><br>

            <dt><a name="atomvalue" type="anchor"><b>Atom Value</b></a></dt>
            <dd><ul>
                    <li>Checker searches for atom values.
                    <li>Fixer offers removing atom values or deleting the atom with value.
                </ul>
                <br><b>Example</b>: delete the atom with value 'isotope'.
                <table border="0">
                    <tbody>
                        <tr>
                            <td>Warning:</td>
                            <td><img src="ex_atomvalue_ch.png" width="273" height="101" alt="ex_atomvalue_ch"/></td>
                        </tr>
                        <tr>
                            <td>Fix:</td>
                            <td><img src="ex_atomvalue_f.png" width="196" height="86" alt="ex_atomvalue_f"/></td>
                        </tr>
                    </tbody>
                </table>

            </dd><br>

            <dt><a name="attached" type="anchor"><b>Attached Data</b></a></dt>
            <dd><ul>
                    <li>Checker searches for attached data.
                    <li>Fixer offers removing attached data or deleting the atom with attached data.
                </ul>
                <br><b>Example</b>: removing attached data (reactant=12) from the oxygen atom.
                <table border="0">
                    <tbody>
                        <tr>
                            <td>Warning:</td>
                            <td><img src="ex_attached_ch.png" width="355" height="129" alt="ex_attached_ch"/></td>
                        </tr>
                        <tr>
                            <td>Fix:</td>
                            <td><img src="ex_attached_f.png" width="212" height="103" alt="ex_attached_f"/></td>
                        </tr>
                    </tbody>
                </table>

            </dd><br>

            <dt><a name="bondangle" type="anchor"><b>Bond Angle</b></a></dt>
            <dd><ul>
                    <li>Checker searches for bonds NOT matching the following rules:
                        <table border="0">
                            <tbody>
                                <tr>
                                    <td><ul><li>Triple bond angle 180&deg; (&plusmn; 0.5 rad)</ul></td>
                                    <td><img src="check_angle1.png" width="152" height="76" alt="check_angle1"/>
                                    </td>
                                </tr>
                                <tr>
                                    <td><ul><li>Double bond angle 120&deg; or 180&deg; (&plusmn; 0.5 rad)</ul></td>
                                    <td><img src="check_angle2.png" width="386" height="108" alt="check_angle2"/>
                                    </td>
                                </tr>
                                <tr>
                                    <td><ul><li>sp<sup>2</sup> atom's bond angles 120&deg;</ul></td>
                                    <td><img src="check_angle3.png" width="118" height="114" alt="check_angle3"/>
                                    </td>
                                </tr>
                                <tr>
                                    <td width="300"><ul><li>sp<sup>3</sup> atom's bond angles 90&deg;<br> <b>or</b> 3 bond angles 120&deg;,
                                        4th bond of an angle of n times 15&deg;;<br> <b>or</b> a bond angle of 120&deg; and two adjacent angles equal</ul></td>
                                    <td><img src="check_angle4.png" width="217" height="291" alt="check_angle4"/>
                                    </td>
                                </tr>
                            </tbody>
                        </table>
                    <li>Fixer offers cleaning the structures by 2D cleaner.
                </ul>
                <br><b>Example</b>: cleaning the molecule.
                <table border="0">
                    <tbody>
                        <tr>
                            <td>Warning:</td>
                            <td><img src="ex_bondangle_ch.png" width="186" height="167" alt="ex_bondangle_ch"/></td>
                        </tr>
                        <tr>
                            <td>Fix:</td>
                            <td><img src="ex_bondangle_f.png" width="152" height="187" alt="ex_bondangle_f"/></td>
                        </tr>
                    </tbody>
                </table>
                Notes: The current version of bond angle checker examines chain bonds of 2D molecules.
                Envelope-shaped cyclic compounds are considered as error.<!--partial clean is not available-->
            </dd><br>

            <dt><a name="bondlength" type="anchor"><b>Bond Length</b></a></dt>
            <dd><ul>
                    <li>Checker searches for bond lengths different than the default setting.
                    <li>Fixer offers cleaning the structures by 2D clean.
                </ul>
                <br><b>Example</b>: cleaning the molecule to adjust bond length.
                <table border="0">
                    <tbody>
                        <tr>
                            <td>Warning:</td>
                            <td><img src="ex_bondlength_ch.png" width="138" height="136" alt="ex_bondlength_ch"/></td>
                        </tr>
                        <tr>
                            <td>Fix:</td>
                            <td><img src="ex_bondlength_f.png" width="124" height="146" alt="ex_bondlength_f"/></td>
                        </tr>
                    </tbody>
                </table>
                Notes: The current version of bond length checker examines chain bonds of 2D molecules.
            </dd><br>

           <dt><a name="chiralflag" type="anchor"><b>Chiral Flag</b></a></dt>
            <dd><ul>
                    <li>Checker searches for set chiral flags in case of non-chiral molecules and
                        for absent chiral flags in case of chiral molecules.
                    <li>Fixer offers removing or setting the chiral flag.
                </ul>
                <br><b>Example</b>: adding chiral flag to a chiral compound not flagged.
                <table border="0">
                    <tbody>
                        <tr>
                            <td>Warning:</td>
                            <td><img src="ex_chiralflag_ch.png" width="130" height="138" alt="ex_chiralflag_ch"/></td>
                        </tr>
                        <tr>
                            <td>Fix:</td>
                            <td><img src="ex_chiralflag_f.png" width="134" height="140" alt="ex_chiralflag_f"/></td>
                        </tr>
                    </tbody>
                </table>
             <!-- Notes:.--></dd><br>

            <dt><a name="coord" type="anchor"><b>Coordination System</b></a></dt>
            <dd><ul>
                    <li>Checker searches for errors in the use of coordinative bonds:
                        <ul><li>2 multicenters connected with a bond</li>
                            <li>coordinated atom is connected to an atom of the same multicenter with a coordinative bond</li>
                            <li>multicenter merged with one of its atoms</li>
                        </ul>
                    <li>Fixer offers deleting the wrong bond or the multicenter
                </ul>
                <br><b>Example</b>: deleting a coordination bond between two multicenters.
                <table border="0">
                    <tbody>
                        <tr>
                            <td>Warning:</td>
                            <td><img src="ex_coord_ch.png" width="111" height="179" alt="ex_coord_ch"/></td>
                        </tr>
                        <tr>
                            <td>Fix:</td>
                            <td><img src="ex_coord_f.png" width="105" height="187" alt="ex_coord_f"/></td>
                        </tr>
                    </tbody>
                </table>
                <!--Notes:.--></dd><br>

            <dt><a name="crosseddouble" type="anchor"><b>Crossed double bond</b></a></dt>
            <dd><ul>
                    <li>Checker searches for crossed double bond types (molecules with unknown or unspecified configuration).
                    <li>Fixer offers cleaning the structures by 2D cleans.
                </ul>
                <br><b>Example</b>: changing a crossed double bond to a wiggly double bond.
                <table border="0">
                    <tbody>
                        <tr>
                            <td>Warning:</td>
                            <td><img src="ex_crossed_ch.png" width="129" height="106" alt="ex_crossed_ch"/></td>
                        </tr>
                        <tr>
                            <td>Fix:</td>
                            <td><img src="ex_crossed_f.png" width="126" height="108" alt="ex_crossed_f"/></td>
                        </tr>
                    </tbody>
                </table>
                Notes: reverse action of wiggly double bond fixing.</dd><br>

                    <dt><a name="doublebond" type="anchor"><b>Double Bond Stereo</b></a></dt>
            <dd>
                <ul>
                    <li>Checker searches for trans double bonds in bridged rings.
                    <li>Fixer offers transforming to cis configuration.
                </ul>
                <br><b>Example</b>: cleaning the molecule.
                <table border="0">
                    <tbody>
                        <tr>
                            <td>Warning:</td>
                            <td><img src="ex_doublebondstereo_ch.png" width="241" height="140" alt="ex_doublebondstereo_ch"/></td>
                        </tr>
                        <tr>
                            <td>Fix:</td>
                            <td><img src="ex_doublebondstereo_f.png" width="205" height="172" alt="ex_doublebondstereo_f"/></td>
                        </tr>
                    </tbody>
                </table>
               

            <dt><a name="explh" type="anchor"><b>Explicit Hydrogen</b></a></dt>
            <dd><ul>
                    <li>Checker searches for explicit hydrogens. Tick options for searching:
                        <ul>
                            <li>lonely</li>
                            <li>isotopic</li>
                            <li>charged</li>
                            <li>radical</li>
                            <li>mapped</li>
                            <li>wegded</li>
                        </ul> explicit hydrogens.
                    <li>Fixer offers removing explicit hydrogens and the ticked special atoms.
                </ul>
                <br><b>Example</b>: removing explicit hydrogen and isotopic hydrogen atoms.
                <table border="0">
                    <tbody>
                        <tr>
                            <td>Warning:</td>
                            <td><img src="ex_explh_ch.png" width="406" height="124" alt="ex_explh_ch"/></td>
                        </tr>
                        <tr>
                            <td>Fix:</td>
                            <td><img src="ex_explh_f.png" width="392" height="97" alt="ex_explh_f"/></td>
                        </tr>
                    </tbody>
                </table>
                <!--Notes:.--></dd><br>

            <dt><a name="isotope" type="anchor"><b>Isotope</b></a></dt>
            <dd><ul>
                    <li>Checker searches for isotopic atoms.
                    <li>Fixer offers changing the isotopic atom to the most abundant natural isotope of that element.
                </ul>
                <br><b>Example</b>: removing isotope information.
                <table border="0">
                    <tbody>
                        <tr>
                            <td>Warning:</td>
                            <td><img src="ex_isotope_ch.png" width="132" height="229" alt="ex_isotope_ch"/></td>
                        </tr>
                        <tr>
                            <td>Fix:</td>
                            <td><img src="ex_isotope_f.png" width="111" height="215" alt="ex_isotope_f"/></td>
                        </tr>
                    </tbody>
                </table>
                Notes: deuterium and tritium are recognized as symbols D and T, respectively as well.</dd><br>

            <dt><a name="missingatommap" type="anchor"><b>Missing Atom Map</b></a></dt>
            <dd><ul>
                    <li>Checker searches for missing atom maps.
                    <li>Fixer offers mapping all atoms in the sketch.
                </ul>
                <br><b>Example</b>: mapping atoms in unmapped molecules.
                <table border="0">
                    <tbody>
                        <tr>
                            <td>Warning:</td>
                            <td><img src="ex_missingmap_ch.png" width="132" height="129" alt="ex_missingatommap_ch"/></td>
                        </tr>
                        <tr>
                            <td>Fix:</td>
                            <td><img src="ex_missingmap_f.png" width="129" height="120" alt="ex_missingatommap_f"/></td>
                        </tr>
                    </tbody>
                </table>
                <!--Notes:.--></dd><br>

            <dt><a name="molcharge" type="anchor"><b>Molecule Charge</b></a></dt>
            <dd><ul>
                    <li>Checker searches molecules in which total charge is not zero.
                    <li>Fixer offers removing the charge by adding or removing hydrogens.
                </ul>
                <br><b>Example</b>: removing charge along with removing a proton.
                <table border="0">
                    <tbody>
                        <tr>
                            <td>Warning:</td>
                            <td><img src="ex_charge_ch.png" width="124" height="169" alt="ex_molcharge_ch"/></td>
                        </tr>
                        <tr>
                            <td>Fix:</td>
                            <td><img src="ex_charge_f.png" width="116" height="168" alt="ex_molcharge_f"/></td>
                        </tr>
                    </tbody>
                </table>
                Notes: charge is not checked in reactions. Charged molecules where no hydrogens can be removed, are to be corrected manually.</dd><br>

            <dt><a name="multicenter" type="anchor"><b>Multicenter</b></a></dt>
            <dd><ul>
                    <li>Checker searches for multicenter drawing.
                    <li>Fixer offers removing the multicenter from the molecule.
                </ul>
                <br><b>Example</b>: removing multicenter.
                <table border="0">
                    <tbody>
                        <tr>
                            <td>Warning:</td>
                            <td><img src="ex_multicenter_ch.png" width="110" height="114" alt="ex_multicenter_ch"/></td>
                        </tr>
                        <tr>
                            <td>Fix:</td>
                            <td><img src="ex_multicenter_f.png" width="108" height="115" alt="ex_multicenter_f"/></td>
                        </tr>
                    </tbody>
                </table>
                <!--Notes:.--></dd><br>

            <dt><a name="overlappingatoms" type="anchor"><b>Overlapping Atoms</b></a></dt>
            <dd><ul>
                    <li>Checker searches for overlapping atoms: atoms closer than the pre-set percentage of the default atom radius.
                    <li>Fixer offers setting or removing the chiral flag.
                </ul>
                <br><b>Example</b>: adding chiral flag to a chiral compound.
                <table border="0">
                    <tbody>
                        <tr>
                            <td>Warning:</td>
                            <td><img src="ex_overlappingatoms_ch.png" width="292" height="128" alt="ex_overlappingatoms_ch"/></td>
                        </tr>
                        <tr>
                            <td>Fix:</td>
                            <td><img src="ex_overlappingatoms_f.png" width="357" height="192" alt="ex_overlappingatoms_f"/></td>
                        </tr>
                    </tbody>
                </table>
                <!--Notes:.--></dd><br>

            <dt><a name="overlappingbonds" type="anchor"><b>Overlapping Bonds</b></a></dt>
            <dd><ul>
                    <li>Checker searches for overlapping bonds: bonds crossing each other or bonds closer to each other than the set minimal value.
                    <li>Fixer offers cleaning the molecule (2D).
                </ul>
                <br><b>Example</b>: cleaning the molecule.
                <table border="0">
                    <tbody>
                        <tr>
                            <td>Warning:</td>
                            <td><img src="ex_overlappingbonds_ch.png" width="212" height="100" alt="ex_overlappingbonds_ch"/></td>
                        </tr>
                        <tr>
                            <td>Fix:</td>
                            <td><img src="ex_overlappingbonds_f.png" width="221" height="92" alt="ex_overlappingbonds_f"/></td>
                        </tr>
                    </tbody>
                </table>
               Notes: bridged polycycles are cleaned as far as their structure allows it, and the overlapping bonds warning will remain.</dd><br>

            <dt><a name="pseudo" type="anchor"><b>Pseudo Atom</b></a></dt>
            <dd><ul>
                    <li>Checker searches for pseudo atoms in the molecule.
                    <li>Fixer offers
                        <ul>
                            <li>converting to abbreviated group if the name is in the abbreviated group list (e.g. Et for ethyl);</li>
                            <li>converting to a carbon atom;</li>
                            <li>deleting atom.</li>
                        </ul>
                </ul>
                <br><b>Example</b>: converting a pseudo atom to a carbon atom.
                <table border="0">
                    <tbody>
                        <tr>
                            <td>Warning:</td>
                            <td><img src="ex_pseudo_ch.png" width="157" height="78" alt="ex_pseudo_ch"/></td>
                        </tr>
                        <tr>
                            <td>Fix:</td>
                            <td><img src="ex_pseudo_f.png" width="163" height="95" alt="ex_pseudo_f"/></td>
                        </tr>
                    </tbody>
                </table>
                <!--Notes:.--></dd><br>

            <dt><a name="queryatom" type="anchor"><b>Query Atom</b></a></dt>
            <dd><ul>
                    <li>Checker searches for query atoms.
                    <li>No fixer for this feature.
                </ul>
                <br><b>Example</b>: finding query atoms.
                <table border="0">
                    <tbody>
                        <tr>
                            <td>Warning:</td>
                            <td><img src="ex_queryatom_ch.png" width="393" height="167" alt="ex_queryatom_ch"/></td>
                        </tr>
                    </tbody>
                </table>
                <!--Notes:.--></dd><br>

            <dt><a name="querybond" type="anchor"><b>Query Bond</b></a></dt>
            <dd><ul>
                   <li>Checker searches for query bonds.
                    <li>No fixer for this feature.
                </ul>
                <br><b>Example</b>: finding query bonds.
                <table border="0">
                    <tbody>
                        <tr>
                            <td>Warning:</td>
                            <td><img src="ex_querybond_ch.png" width="484" height="160" alt="ex_querybond_ch"/></td>
                        </tr>
                     </tbody>
                </table>
                <!--Notes:.--></dd><br>

            <dt><a name="radical" type="anchor"><b>Radical</b></a></dt>
            <dd><ul>
                    <li>Checker searches for radical information on molecules.
                    <li>Fixer offers removing the radical information.
                </ul>
                <br><b>Example</b>: removing wrong radical from acetate.
                <table border="0">
                    <tbody>
                        <tr>
                            <td>Warning:</td>
                            <td><img src="ex_radical_ch.png" width="127" height="111" alt="ex_radical_ch"/></td>
                        </tr>
                        <tr>
                            <td>Fix:</td>
                            <td><img src="ex_radical_f.png" width="118" height="105" alt="ex_radical_f"/></td>
                        </tr>
                    </tbody>
                </table>
                <!--Notes:.--></dd><br>

        <dt><a name="reactionmap" type="anchor"><b>Reaction Map</b></a></dt>
            <dd><ul>
                    <li>Checker searches for incomplete reaction map.
                        A reaction with two or less atom maps (both on the reactant and the product side)
                        is considered an incompletely mapped reaction.
                    <li>Fixer offers mapping the reaction.
                </ul>
                <br><b>Example</b>: mapping a partially mapped reaction.
                <table border="0">
                    <tbody>
                        <tr>
                            <td>Warning:</td>
                            <td><img src="ex_reactionmap_ch.png" width="539" height="126" alt="ex_reactionmap_ch"/></td>
                        </tr>
                        <tr>
                            <td>Fix:</td>
                            <td><img src="ex_reactionmap_f.png" width="554" height="134" alt="ex_reactionmap_f"/></td>
                        </tr>
                    </tbody>
                </table>
                <!--Notes:.--></dd><br>

            <dt><a name="3d" type="anchor"><b>Three Dimension</b></a></dt>
            <dd><ul>
                    <li>Checker searches for 3rd dimension (Z) coordinates.
                    <li>Fixer offers 2D cleaning.
                </ul>
                <br><b>Example</b>: cleaning the cyclohexane in 2D.
                <table border="0">
                    <tbody>
                        <tr>
                            <td>Warning:</td>
                            <td><img src="ex_3d_ch.png" width="276" height="187" alt="ex_3d_ch"/></td>
                        </tr>
                        <tr>
                            <td>Fix:</td>
                            <td><img src="ex_3d_f.png" width="153" height="165" alt="ex_3d_f"/></td>
                        </tr>
                    </tbody>
                </table>
                <!--Notes:.--></dd><br>

            <dt><a name="valence" type="anchor"><b>Valence</b></a></dt>
            <dd><ul>
                    <li>Checker searches for valence errors.
                    <li>Fixer offers removing explicit hydrogens if applicable.
                </ul>
                <br><b>Example</b>: removing a hydrogen from the ammonium ion with no charge set.
                <table border="0">
                    <tbody>
                        <tr>
                            <td>Warning:</td>
                            <td><img src="ex_valence_ch.png" width="267" height="140" alt="ex_valence_ch"/></td>
                        </tr>
                        <tr>
                            <td>Fix:</td>
                            <td><img src="ex_valence_f.png" width="224" height="131" alt="ex_valence_f"/></td>
                        </tr>
                    </tbody>
                </table>
                Notes: valence errors with no removable hydrogens have to be corrected manually.</dd><br>

            <dt><a name="wedge" type="anchor"><b>Wedge</b></a></dt>
            <dd><ul>
                    <li>Checker searches for superfluous wedge bonds.
                    <li>Fixer offers removing all wedge bonds and replacing them with a single bond.
                </ul>
                <br><b>Example</b>:
                <table border="0">
                    <tbody>
                        <tr>
                            <td>Warning:</td>
                            <td><img src="ex_wedge_ch.png" width="156" height="155" alt="ex_wedge_ch"/></td>
                        </tr>
                        <tr>
                            <td>Fix:</td>
                            <td><img src="ex_wedge_f.png" width="156" height="153" alt="ex_wedge_f"/></td>
                        </tr>
                    </tbody>
                </table>
                Notes: some symmetric structures are not recognized by the checker.</dd><br>
        </dl>

            <dt><a name="wigglydouble" type="anchor"><b>Wiggly Double Bond</b></a></dt>
            <dd><ul>
                    <li>Checker searches for wiggly double bond (molecules with unknown or unspecified configuration).
                    <li>Fixer offers changing to crossed double bond type.
                </ul>
                <br><b>Example</b>: changing a wiggly double bond to a crossed double bond.
                <table border="0">
                    <tbody>
                        <tr>
                            <td>Warning:</td>
                            <td><img src="ex_wiggly_ch.png" width="217" height="193" alt="ex_wiggly_ch"/></td>
                        </tr>
                        <tr>
                            <td>Fix:</td>
                            <td><img src="ex_wiggly_f.png" width="226" height="192" alt="ex_wiggly_f"/></td>
                        </tr>
                    </tbody>
                </table>
                Notes: reverse action of crossed double bond fixing.</dd><br>
        </dl>

    </body>
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